I'm trying to backup my NTFS Windows disk to another NTFS disk. Using rsync on Cygwin, what options should I use so I don't have any permission problems in the future? I don't plan on restoring the entire OS, just my personal user files and preferences after I change OS.

rsync --verbose --acls --archive --hard-links --delete "/cygdrive/c" "/cygdrive/w/my-backup/"

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    Is there a reason you can't use robocopy? robocopy c:\ w:\my-backup /s/e /copyall /a+:a /dcopy:t – Aaron Mason Sep 5 '16 at 4:28
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    You might also consider using parameters -AXogt but look over linux.die.net/man/1/rsync for full detail and to ensure you don't overlap, etc. I agree... Robocopy is a good tool to use with Windows for this type of task. – Pimp Juice IT Sep 5 '16 at 4:46
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    I agree on robocopy. It is much faster for local usage than rsync specially with /MT option. – matzeri Sep 5 '16 at 9:55
  • @AaronMason I have an entire workflow set up on bash. @ matzeri How is robocopy faster if rsync already max out my throughput? Did you tested it both at the same pc and same job? It's so fast for me that any speed gains would be negligible. Maybe you're talking about file comparison times. But thanks for the suggestion! – user168623 Sep 5 '16 at 15:09
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    If it's just a small VM & for local files only & for local user accounts, then it should be rather easy to test with a test VM & then create a new dummy account & see what you get. I normally control NTFS security with security groups & as long as the group's SID is tied to the ACLS, then any user account (including new ones) will be allowed to access the data per the ACL security configuration. Look over superuser.com/questions/69620/rsync-file-permissions-on-windows here for potential answer but it looks like you should include --p as well... see ==> linux.die.net/man/1/rsync – Pimp Juice IT Sep 6 '16 at 0:31

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